Variant report

Variant	rs16957085
Chromosome Location	chr17:46532956-46532957
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:46530850..46533321-chr17:46662351..46664282,2	K562	blood:
2	chr17:46532678..46534272-chr17:46625300..46627846,2	K562	blood:
3	chr17:46532737..46535111-chr17:46677941..46680284,2	K562	blood:
4	chr17:46532115..46533858-chr17:46568103..46570537,2	MCF-7	breast:
5	chr17:46532772..46535087-chr17:46626346..46628551,2	K562	blood:

Variant related genes	Relation type
ENSG00000233101	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10514944	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];0.94[TSI][hapmap];0.89[AFR][1000 genomes]
rs1396869	0.88[ASN][1000 genomes]
rs16954324	0.87[AFR][1000 genomes]
rs16955960	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes]
rs16956001	0.89[AFR][1000 genomes]
rs16956501	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[JPT][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16957299	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs17621689	1.00[CEU][hapmap];0.89[AFR][1000 genomes]
rs17623125	0.89[AFR][1000 genomes]
rs17623416	1.00[CEU][hapmap];0.89[AFR][1000 genomes]
rs17623518	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];1.00[AFR][1000 genomes]
rs17694092	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.89[AFR][1000 genomes]
rs17694168	0.89[AFR][1000 genomes]
rs17694404	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs17694670	0.89[AFR][1000 genomes]
rs2036521	0.89[AFR][1000 genomes]
rs2175156	1.00[AFR][1000 genomes]
rs2271264	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34463696	0.85[ASN][1000 genomes]
rs3760513	0.81[CHB][hapmap]
rs3809744	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55641965	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55751709	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55765969	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55912545	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56011283	0.87[ASN][1000 genomes]
rs56103412	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56311919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56371910	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72825596	0.89[AFR][1000 genomes]
rs72827810	0.89[AFR][1000 genomes]
rs72827825	0.89[AFR][1000 genomes]
rs72827851	0.89[AFR][1000 genomes]
rs72827854	0.89[AFR][1000 genomes]
rs72827869	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72827873	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72827897	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs9899997	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9907565	1.00[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9913716	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833469	chr17:46491849-46709406	Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	349 gene(s)	inside rSNPs	diseases
2	esv3420538	chr17:46504944-46861553	Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	369 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16957085	HOXB2	cis	multi-tissue	Pritchard
rs16957085	SNX11	cis	multi-tissue	Pritchard

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46528800-46535200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr17:46529000-46535400	Enhancers	Fetal Thymus	thymus
3	chr17:46529200-46533800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr17:46531200-46533000	Weak transcription	K562	blood
5	chr17:46531400-46533800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:46531400-46534400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr17:46531400-46534400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr17:46531600-46533000	Enhancers	Thymus	Thymus
9	chr17:46531600-46534200	Enhancers	Primary T cells from cord blood	blood
10	chr17:46531600-46534200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr17:46531600-46534200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
12	chr17:46531600-46534200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr17:46531600-46534400	Enhancers	Primary T cells fromperipheralblood	blood
14	chr17:46531600-46534400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr17:46531600-46534400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr17:46531800-46533800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr17:46531800-46534200	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr17:46531800-46534200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr17:46531800-46534200	Enhancers	Primary T helper cells PMA-I stimulated	--
20	chr17:46531800-46534400	Enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr17:46532000-46535200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr17:46532200-46533000	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr17:46532200-46534200	Weak transcription	Primary B cells from cord blood	blood
24	chr17:46532800-46533600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr17:46532800-46533800	Weak transcription	Primary B cells from peripheral blood	blood
26	chr17:46532800-46534400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links